Contacts of the strand formed by residues 980 - 989 (chain A) in PDB entry 3KZ1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 980 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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975A ARG 3.9 0.2 - - - -
976A ILE* 3.2 41.7 + - + +
977A SER* 3.4 21.1 + - - +
978A LYS 3.1 4.3 - - - +
979A ASP* 1.3 83.7 - - - +
981A THR* 1.3 68.8 + - - +
1010A LYS 6.1 1.3 - - - +
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Residues in contact with THR 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A THR* 4.0 24.2 - - + -
974A TRP 3.4 5.6 - - - +
975A ARG* 4.1 23.8 - - - +
976A ILE* 5.0 1.8 - - - -
979A ASP* 5.4 1.7 - - - -
980A LYS* 1.3 82.9 - - - +
982A LEU* 1.3 64.7 + - - +
983A ASP* 5.4 1.1 - - - -
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Residues in contact with LEU 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974A TRP* 2.8 58.2 + - + +
976A ILE* 4.8 11.0 - - + -
981A THR* 1.3 77.0 - - - +
983A ASP* 1.3 78.7 + - - +
984A LEU* 3.6 11.6 + - + -
997A GLN* 3.5 35.9 - - + +
1008A HIS* 3.8 24.2 - - + +
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Residues in contact with ASP 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A LEU 4.1 3.1 - - - -
973A THR* 3.2 29.7 + - - +
981A THR* 5.4 0.9 - - - -
982A LEU* 1.3 87.6 + - - +
984A LEU* 1.3 61.6 + - - +
997A GLN* 4.5 8.3 - - - +
998A LYS 5.0 1.7 + - - -
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Residues in contact with LEU 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A PRO* 3.5 8.5 - - - +
972A LEU 3.0 29.7 + - - +
974A TRP* 3.7 37.0 - - + -
982A LEU* 4.1 20.4 - - + +
983A ASP* 1.3 80.1 - - - +
985A HIS* 1.3 66.7 + - - +
986A VAL* 4.1 2.7 - - + +
995A LEU* 3.8 35.0 - - + -
996A LEU 3.5 27.6 - - - +
997A GLN* 4.0 5.8 - - + +
998A LYS* 6.2 1.3 - - - -
1008A HIS* 5.1 6.5 - - - +
1059A LEU* 4.3 6.1 - - + -
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Residues in contact with HIS 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A TYR* 4.1 10.8 + + - -
969A GLU* 3.1 33.0 + - + -
970A GLY* 3.6 28.0 + - - -
971A PRO* 4.2 7.2 - - + -
984A LEU* 1.3 76.6 - - - +
986A VAL* 1.3 61.3 + - - +
987A LEU* 3.6 19.3 - - + +
996A LEU* 2.9 43.6 + - + +
998A LYS* 4.7 27.6 - - + -
1003A LEU* 5.6 5.6 - - + +
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Residues in contact with VAL 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A GLU* 3.3 6.8 - - - +
970A GLY 2.9 36.4 + - - +
972A LEU* 3.2 39.5 - - + +
984A LEU* 5.2 1.8 - - + -
985A HIS* 1.3 76.8 + - - +
987A LEU* 1.3 67.2 + - - +
993A LEU* 3.7 34.1 - - + -
994A VAL 3.6 11.7 - - - +
995A LEU* 4.0 18.6 - - + -
1059A LEU* 5.5 0.4 - - + -
1070A TRP* 3.8 10.4 - - + -
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Residues in contact with LEU 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933A LEU* 4.6 7.6 - - + -
936A TYR* 3.9 17.9 - - + -
961A LEU* 4.2 24.7 - - + -
966A MET* 4.0 5.4 - - - -
968A HIS 3.9 2.9 - - - +
969A GLU* 3.8 16.8 - - + +
985A HIS* 3.6 31.0 - - + +
986A VAL* 1.3 76.9 - - - +
988A LEU* 1.3 60.7 + - - +
989A LEU* 3.9 9.9 + - + -
992A LEU 4.0 0.2 - - - +
993A LEU* 3.5 9.0 - - - +
994A VAL* 3.1 44.2 + - + +
996A LEU* 3.7 27.4 - - + -
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Residues in contact with LEU 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A MET* 3.7 2.9 - - - +
967A ILE* 2.8 33.9 + - + -
968A HIS* 2.9 41.2 + - + +
986A VAL* 4.2 0.4 - - - +
987A LEU* 1.3 73.6 - - - +
989A LEU* 1.3 72.7 + - - +
992A LEU 4.1 2.5 - - - +
993A LEU* 4.1 7.4 - - + -
1028A LEU* 4.3 9.0 - - + -
1070A TRP* 4.2 8.9 - - + -
1073A LEU* 3.9 22.0 - - + +
1074A LEU* 3.7 32.5 - - + -
1077A ALA* 3.8 21.8 - - + -
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Residues in contact with LEU 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933A LEU* 4.1 21.5 - - + -
961A LEU* 4.0 16.2 - - + +
964A ARG* 4.3 20.4 - - + -
965A LYS 3.4 18.4 - - - +
966A MET* 3.8 17.5 - - + +
967A ILE* 3.7 4.7 - - - +
987A LEU* 4.7 5.6 - - + -
988A LEU* 1.3 81.5 - - - +
990A GLU* 1.3 68.3 + - - +
991A ASP* 3.2 1.9 + - - +
992A LEU* 2.8 35.7 + - + +
994A VAL* 3.7 28.3 - - + -
1028A LEU* 3.3 17.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il